Since childhood, Kyouya Daiguuji showed an almost supernatural talent as inventor, but everyone sees him as an eccentric gymnastics buff instead.
Bullied and/or ignored by his (female) schoolmates, and more than a little envious of the popularity his father (the school principal and the protagonist of the prequel) enjoys, Kyouya finally blews up and founds the secret "2nd Division of Science Club".
Under the guise of Commander Dark and with the help of his inventions and (duped) minions, Kyouya starts a one-man war against his tormentors, and only total subjugation of all the (females in the) school will be enough for his hurt ego!!